Prime Minister Tony Abbott has taken a conciliatory approach to his talks with Indonesian president Susilo Bambang Yudhoyono.

In Jakarta, Mr Abbott said Australia had made mistakes in its relationship with Indonesia in the past, and called on both countries to make a new start in the areas of agriculture and food security in particular.

"There have been times, I'm sorry to say, when Australia must have tried your patience; when we put sugar on the table for people smugglers, or cancelled the live cattle trade in panic at a TV program," Mr Abbott said.

"I am confident that these will soon seem like out-of-character aberrations."

Referring specifically to the former Federal Government's 2011 decision to temporarily suspend the live cattle trade to Indonesia over animal welfare concerns, Mr Abbott indicated that kind of action was off the table in the future.

"Never again should this country take action which jeopardises the food supply of such a friend and partner as Indonesia is," Mr Abbott said, pointing to the contingent of business leaders travelling with him in Jakarta, as evidence of the "desire of the Australian people to build a much stronger, much more broadly based, and much more dynamic economic relationship, based on greater trade and investment, in the years to come."

The Australian Livestock Exporters Council has welcomed the Prime Minister's comments.

"I certainly don't see it in any way as sweeping under the carpet those animal welfare improvements that industry needs to make, but it certainly fulfills the brief that we had set for the Prime Minister.

"It signals a return to policy settings that provide certainty and stability for producers and exporters," she said.

"I don't think industry will ever put behind it what happened in 2011, for a variety of reasons, but one is that it's a reminder that if we don't get the welfare conditions right, that government has that power.

"We are continuing to do everything we can to ensure that kind of circumstance never happens again. We've got a long way to go, but we're striving for continual improvement."